ONE-BAG
You run everything yourself
Every topic is a short theory block followed straight away by a practical. Under two hours between an idea and your own hands on it, coffee break included.
Funded by the European One Health Association
From raw reads to a tree you can defend.
A hands-on course for people who sequence bacteria and want to analyse those genomes themselves. Four days in València. Free at an EOHA full member institution, 300 € for everyone else.
Dates14 to 17 December 2026
WhereI2SysBio, València
PlacesLimited
Fee300 € (0 for full members)
Travel grantsUp to 600 €
Course starts in
4days, from raw reads to phylogeny
16sessions, half of them at the keyboard
5trainers, and never fewer than two in the room
0 / 300 €free at an EOHA full member institution
Why come
Most courses stop at the tutorial dataset
This one is about what comes next: picking a method, reading what it gives you, and defending the conclusion in front of people who will act on it.
Two trainers in the room, all four days
Five of them in total, so the pairing changes with the topic. When a command fails at 16:40 you are not waiting until the next break to have it looked at.
Aimed at what the room works on
Everyone runs the same prepared datasets, so the whole room moves together. What you tell us you sequence steers the examples, the edge cases and the questions we spend time on.
Nothing to install, nothing to lose
An account on the institute's cluster with every tool ready, and a GitHub repository of slides, data and scripts that stays yours afterwards.
What you learn
Eight things you will be able to do
In the order a genome travels through the analysis, which is also the order of the four days.
Judge your reads
Quality control of short and long reads, and knowing what to throw away.
Day 1Call SNPs properly
Reference-based and core-genome SNP analysis, and when each one applies.
Day 1Assemble a genome
Short-read, long-read and hybrid assembly, and which one your question needs.
Day 2Spot a bad assembly
N50, completeness and contamination, and when not to trust the result.
Day 2Annotate and compare
Genome annotation, and the core and accessory split that a pan-genome reveals.
Day 3Investigate an outbreak
Comparative genomics for outbreaks and surveillance, disagreements included.
Day 3Type strains and find AMR
MLST, cgMLST, resistance genes and plasmids, discrepancies and all.
Day 4Build and read a tree
Phylogenies with the time, place and host metadata that make them mean something.
Day 4
The four days
Mornings for the idea, afternoons for the data
09:30 to 17:30, with two coffee breaks and lunch on site every day. One row below is fifteen minutes, so every block is drawn at the length it lasts.
Scroll sideways for the other three days
Mon 14 DecReads, QC and SNPs
Tue 15 DecAssembly and its quality
Wed 16 DecAnnotation and pan-genome
Thu 17 DecTyping, AMR and trees
09:30
10:45
11:15
13:00
14:00
15:15
15:45
17:30
Theory 1VLCS
Understanding raw reads and QCTheory 3FCCS
De novo assembly and assembly QCTheory 5MCPR
Core, accessory and pan-genomeTheory 7FCCS
MLST, cgMLST, AMR and plasmidsCoffee
Practical 1VLCS
Raw read QC and read processingPractical 3FCCS
Assembly and quality evaluationPractical 5MCPR
Annotation and pan-genomePractical 7FCCS
Typing, AMR and plasmid annotationLunch, on site, with the trainers
Theory 2VLCS
Core-genome and reference-based SNPsTheory 4FCMC
Assembly case studiesTheory 6FCPR
Aligning assembliesTheory 8MCPR
Phylogenetic treesCoffee
Practical 2VLCS
SNP calling and SNP alignmentPractical 4FCMC
Reading and rescuing assembly outputPractical 6FCPR
Outbreak case studiesPractical 8MCPR
Tree building and visualisation
Theory
Practical
Break, included
Raw reads, quality control and SNP analysis
Morning
Theory. Understanding raw reads and quality control.
Practical. Raw read QC and read processing.
FastQCMultiQCnanoQCfastpTrimmomatic
Afternoon
Theory. Core-genome and reference-based SNP analysis.
Practical. SNP calling and SNP alignment.
Snippysnp-sitesvSNP 3.0
Taught byVLVíctor LorenteCSCarlos Serna
De novo assembly and assembly quality control
Morning
Theory. Assembly and its quality: N50, genome size, GC content, completeness, contamination.
Practical. Assembling processed reads and evaluating the result.
SPAdesUnicyclerQUASTCheckM2BUSCO
Afternoon
Theory. Case studies in bacterial genome assembly.
Practical. Interpreting results and identifying problematic assemblies.
Assembly graphsContamination screening
Taught byFCFrancesc CollCSCarlos SernaMCMireia Coscollá
Annotation, pan-genome and genome comparisons
Morning
Theory. Core genome, accessory genome and pan-genome analysis.
Practical. Genome annotation and pan-genome calculation.
ProkkaBaktaRoaryPanaroo
Afternoon
Theory. Aligning reference-based and non-reference-based assemblies.
Practical. Case studies in bacterial genome outbreaks.
MauveSKA2wfmash
Taught byMCMireia CoscolláPRPaula RuizFCFrancesc Coll
Typing, AMR, plasmids and phylogenetics
Morning
Theory. MLST, cgMLST, AMR databases and plasmids.
Practical. Bacterial typing, AMR detection and plasmid annotation.
mlstchewBBACAAMRFinderPlusABRicatePlasmidFinderMOB-suite
Afternoon
Theory. Phylogenetic tree construction and visualisation.
Practical. Phylogenetic reconstruction and tree visualisation.
RAxMLIQ-TREEiTOLMicroreact
Taught byFCFrancesc CollCSCarlos SernaMCMireia CoscolláPRPaula Ruiz
Who teaches
Five trainers, four institutions
Assembled with a One Health mindset: microbial genomics, public health surveillance, antimicrobial resistance and animal health, all in the same room.
MCMireia Coscollá Devís
Group leader, course director
I2SysBio, CSIC and University of Valencia. PhD in Evolutionary Biology.
0000-0003-0752-0538 Days 2, 3, 4
FCFrancesc Coll
Group leader
Institute of Biomedicine of Valencia, CSIC. PhD in Microbial Genomics, LSHTM.
0000-0002-7882-2325 Days 2, 3, 4
PRPaula Ruiz Rodríguez
PhD candidate
I2SysBio, CSIC and University of Valencia. MSc in Bioinformatics.
0000-0003-0727-5974 Days 3, 4
CSCarlos Serna Bernaldo
Assistant Professor
VISAVET and Faculty of Veterinary Medicine, Complutense University of Madrid.
0000-0002-6008-6024 Days 1, 2, 4
VLVíctor Lorente Leal
Assistant Professor
VISAVET and Faculty of Biological Sciences, Complutense University of Madrid.
0000-0003-4096-0885 Day 1
Your machine
Serious hardware,
Serious hardware,
nothing to install
An account each on Garnatxa, the institute's compute cluster. You reach it over SSH from your own laptop, so there is nothing to install and nothing to carry. Bring a laptop, connect, start computing.
608CPU cores
1,216threads
15 TBRAM across the cluster
3.5 PBdistributed storage
What you take home
- A GitHub repository with every slide, exercise, dataset and script.
- Access before and after, so you can prepare and repeat the analyses later.
- Command lines you can rerun on your own infrastructure, not black-box clicking.
- A certificate of attendance.
Where
Four days in València
At I2SysBio, on the Science Park campus in Paterna. December here averages 17 °C by day, the sun sets at 17:38, and sessions finish at 17:30 with the city still open.
Click the map to zoom
What it costs
Nothing for EOHA full members. 300 € for everyone else.
Funded by the European One Health Association with co-funding from the host institute, which is what makes the places free for people at its full member institutions. Everyone else pays a registration fee that covers exactly the same four days.
0 €
at an EOHA full member
institution. Nothing invoiced
to your lab, ever.
institution. Nothing invoiced
to your lab, ever.
300 €
for everyone else, due within a
week of your place being confirmed.
week of your place being confirmed.
The 300 € is due within one week of your place being confirmed. Tell us if that week is difficult and we will work around it. After a week with no word, the place goes to the next person on the list.
- Sixteen sessions with two trainers in the room4 days
- Your own account on the Garnatxa cluster608 cores
- Slides, exercises, datasets and scripts, yours to keepGitHub
- Two coffee breaks and lunch, on site, every day8 + 4
- Certificate of attendanceafter
Getting there
up to 300 €From Spain
Travel and accommodation for participants at an EOHA full member institution based in Spain.
up to 600 €From abroad
Travel and accommodation for participants at an EOHA full member institution outside Spain.
Travel grants are only available for EOHA full member institutions and can be requested directly in the application form by briefly explaining, in a couple of sentences, what receiving the grant would mean to your research or institution. There will be no second deadline or additional application round, and decisions will reach all selected attendees during the second week of October to allow enough time to book flights at a reasonable price.
At a full member institution there is no registration fee, and travel and accommodation are the only things you cover yourself, and only if you do not receive a grant. Everyone else covers the 300 € as well.
How to apply
One form, your CV, and it closes 1 October.
Places are limited*, and some of them are held for people at EOHA full member institutions. Anyone who works with bacterial genomes can apply.
*Based on the number of applications, the number of participants per institute may be limited to ensure a balanced representation.
Applications closed on 1 October 2026. Everyone who applied hears in the second week of October, and the course runs 14 to 17 December.
Fill in the form
Who you are, what you sequence, how comfortable you are on the command line. Then two short answers: what you would use bacterial genomics for, and what a travel grant would make possible. Your CV at the end.
We select
Those two answers are what decides it: how relevant the course is to your work, and the difference it will make. Worth the ten minutes.
You are offered a place
Confirmation and the travel grant decision arrive together, with the fee if one applies to you.
You confirm within a week
Say yes and pay within the week. If that week is awkward, tell us and we will work around it; it is silence that passes the place to the next person. Then the preparation material and your cluster login follow.
Applications open
Not first come first served, so applying early does not put you ahead. It does mean you will not forget.
Applications close
Last day for the form and the CV. Grant requests are part of it, so there is no second application.
We confirm it runs
Everyone is told whether the course goes ahead, before anybody books travel.
Offers go out
Offers and grant decisions go out, and the fee is asked for.
The fee falls due
One week after a place is confirmed. A place that goes unpaid passes on, early enough for the next person to book.
Four days in València
You arrive with your questions and a laptop. The cluster account is waiting.
You bring your own laptop
This is required. Any operating system, any age, as long as it connects to Wi-Fi and can open a terminal to connect over SSH. On Windows that means Windows Terminal or WSL, both free. All the computing runs on the cluster you log in to, so your laptop does not need to be powerful and you install nothing on it.
You are comfortable in a terminal
Basic Linux command line only. Moving between directories, running a program with arguments, reading its output. No Python, no R, no programming experience. We send preparatory material to everyone who registers.
A small group, and a minimum to run
The course only runs if enough people are selected. That is decided in the first week of October, before anybody is asked for money or books travel, and everyone who applied is told either way.
What happens to what you send
Your application is read by the five trainers and by nobody else. It is not shared with the funder, with the host institute's administration or with anybody outside that group, and it is not used to contact you about anything other than this course. The one exception is a registration fee, if you owe one: to invoice it, the host institute's finance office is given your name and your institution's billing details, and nothing else from what you sent. The form and the files it collects sit in Google Forms and Google Drive, and everything is deleted once the course has run and the certificates are out. Write to us at any point and we take your application out earlier, whether or not the deadline has passed.
Full membership decides both what you pay and whether you can ask for a grant
Anyone can apply for a place. What working at a full member institution of the European One Health Association changes is the money: the course is free instead of 300 €, and the travel grants are open to you. So check rather than assume: there are 27 full members in 17 countries, and some are whole national research bodies rather than single centres, so you may be inside one without knowing it. From Spain, both CSIC and VISAVET at the Complutense University of Madrid are full members.
See the 27 full member institutions
Austria
- Austrian Agency for Health and Food Safety (AGES)
- University of Veterinary Medicine, Vienna (Vetmeduni Vienna)
Belgium
- SCIENSANO
Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen (KU)
- National Food Institute, Technical University of Denmark (DTU)
- Statens Serum Institut (SSI)
Finland
- Finnish Food Authority (RUOKA)
France
- French Agency for food, environmental and occupational health and safety (ANSES)
Germany
- Bundesinstitut für Risikobewertung (BfR)
Ireland
- Central Veterinary Research Laboratory (CVRL)
- University of Galway
Italy
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER)
- Italian National Institute of Health (ISS)
Latvia
- Institute of Food Safety, Animal Health and Environment (BIOR)
Netherlands
- National Institute for Public Health and the Environment (RIVM)
- Wageningen Bioveterinary Research (WBVR)
- Wageningen Food Safety research (WFSR)
Norway
- Norwegian Institute of Public Health (FHI)
- Norwegian Veterinary Institute (NVI)
Poland
- National Veterinary Research Institute (PIWET)
Portugal
- Instituto Nacional de Saúde Dr. Ricardo Jorge (INSA)
Slovenia
- University of Ljubljana, Faculty of Veterinary Medicine
Spain
- Agencia Estatal Consejo Superior de Investigaciones Cientificas (CSIC)
- Universidad Complutense Madrid, Centre for Veterinary Health Surveillance (VISAVET)
Sweden
- Swedish Veterinary Agency (SVA)
United Kingdom
- Animal and Plant Health Agency (APHA)
- University of Surrey (UoS)
27 full members in 17 countries. The list on onehealthassoc.eu is the one that governs.
It takes a minute, and it decides both what the course costs you and whether you can ask for the travel money on the same form.
14 to 17 December 2026 · València
Four days in December.
Four days in December.
Bring your questions.
Four days, five trainers, and a tree at the end of it that is yours to defend.
Questions
Before you apply
Do I need to know how to program?
No. You do need to be comfortable on the Linux command line: moving between directories, running a program with arguments, reading its output. We send a list of short preparatory courses to everyone who registers.
What do I need to bring?
Your own laptop. That part is not optional, and we cannot lend you one. Any operating system and any age is fine, as long as it connects to Wi-Fi and can open a terminal to connect over SSH. On Windows that means Windows Terminal or WSL, both free. Everything runs on the cluster you log in to, so nothing is installed on your machine and it does not need to be powerful.
Can I work on my own data?
Bring it, and bring the questions that come with it. What the practicals will not do is run on a different dataset for everyone: they use prepared ones, so the whole group moves at the same pace and nothing stalls on a file that will not assemble. That is a deliberate choice, and it is what lets you finish four days with results you can compare against everyone else's.
Around that, your own data is welcome. The trainers are in the room at every break and at lunch, and what you tell us on the form about your organisms feeds into which examples and problem cases we use.
Is it free?
It is free for people at an EOHA full member institution: tuition, compute, materials and catering are covered by the association and the host institute, and nothing is invoiced to your lab. For everyone else the registration fee is 300 €, and it buys exactly the same four days. Travel and accommodation are yours either way, unless you get one of the travel grants, in which case you are reimbursed up to the limit for that grant.
The travel grants are for people at EOHA full member institutions, so check the list of full members before you write them off: whole research councils are on it, and you may be inside one without knowing.
When do I pay, and what if I cannot pay in time?
Your place is confirmed in the second week of October, and the fee is due within one week of that. That week is short on purpose: mid December is an expensive time to fly to Spain and beds go early, so a place sitting unpaid is a place somebody else cannot plan around.
If the week does not work for you, write to us and say so. A finance office that needs three weeks to move an invoice is a reason to give you three weeks, not a reason to lose the place. What costs you the place is silence: after a week with no word from you, it goes to the next person on the list.
I have paid and now I cannot come. What happens?
Write to us and the place can go to a colleague instead, so the seat is not wasted and neither is your money. What we cannot do is refund the fee once it is paid.
Is there a waiting list?
Yes. There are usually more good applications than places, so anyone who is not selected is told in the same message whether they are next in line. The places held for full member institutions and the open ones are filled separately, so each has its own queue, and a place that is not taken up is offered straight away to the first person waiting for that kind of place.
Who can apply?
Anyone who sequences bacteria and wants to analyse those genomes, whatever their career stage and wherever they work. What decides it is how relevant the course is to your work and the difference it is likely to make. Being at an EOHA full member institution is what decides the money: no fee instead of 300 €, and the travel grants. Both are settled on the same form.
What if too few people apply?
The course needs a minimum number of people to run, and that is settled in the first week of October, before anybody is asked for money. If we do not get there we tell everyone who applied as early as we can, so nobody books a flight for a course that will not happen.
Do I get a certificate?
Yes, after the course, stating 24 hours of teaching: six hours a day across the four days, which is the figure most training records ask for. You will also be asked for a short evaluation, which feeds into the next EOHA training.
What language is the course taught in?
English, all four days: the slides, the exercises and the questions. You do not need it to be fluent, and the trainers between them also speak Spanish and Catalan if a concept refuses to land in English.
How do I ask something that is not answered here?
The application form ends with a free text box. Write the question there and we answer it before the deadline, whether or not you go on to apply.
Where does the name ONE-BAG come from?
From the logo above: ONE Health BActerial Genomics. The coloured letters give it away.
ONEOne Health
BABacterial
GGenomics
Everything you need for four days of bacterial genomics, packed into one bag.
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